def importFromDICOMWeb(dicomWebEndpoint, studyInstanceUID, seriesInstanceUID=None, accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Example usage:
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
"""
from dicomweb_client.api import DICOMwebClient
import random
if accessToken is None:
client = DICOMwebClient(url = dicomWebEndpoint)
else:
client = DICOMwebClient(
url = dicomWebEndpoint,
headers = { "Authorization": "Bearer {}".format(accessToken) },
)
seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if not seriesInstanceUID is None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
fileNumber = 0
for currentSeriesInstanceUID in seriesInstanceUIDs:
instances = client.retrieve_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime().toString("yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instance in instances:
filename = outputDirectoryPath + "/" + str(fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
slicer.app.processEvents()
importDicom(outputDirectoryPath)
return seriesInstanceUIDs
def onExport(self):
# set up the threeDWidget at the correct render size
layoutManager = slicer.app.layoutManager()
oldLayout = layoutManager.layout
threeDWidget = layoutManager.threeDWidget(0)
threeDWidget.setParent(None)
threeDWidget.show()
geometry = threeDWidget.geometry
size = self.sizes[self.sizeSelector.currentText]
threeDWidget.threeDController().visible = False
threeDWidget.setGeometry(geometry.x(), geometry.y(), size["width"], size["height"])
# set up the animation nodes
viewNode = threeDWidget.threeDView().mrmlViewNode()
animationNode = self.animationSelector.currentNode()
sequenceBrowserNode = slicer.util.getNode(animationNode.GetAttribute('Animator.sequenceBrowserNodeID'))
sequenceNodes = vtk.vtkCollection()
sequenceBrowserNode.GetSynchronizedSequenceNodes(sequenceNodes, True) # include master
sequenceNode = sequenceNodes.GetItemAsObject(0)
frameCount = sequenceNode.GetNumberOfDataNodes()
tempDir = qt.QTemporaryDir()
fileExtension = self.fileFormats[self.fileFormatSelector.currentText]
# perform the screen capture and video creation
from ScreenCapture import ScreenCaptureLogic
logic = ScreenCaptureLogic()
logic.captureSequence(
viewNode,
sequenceBrowserNode,
0, frameCount-1, frameCount,
tempDir.path(),
"Slicer-%04d.png")
logic.createVideo(
60,
"-pix_fmt yuv420p",
tempDir.path(),
"Slicer-%04d.png",
self.outputFileButton.text+fileExtension)
# reset the view
threeDWidget.threeDController().visible = True
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFinalView) ;# force change
layoutManager.setLayout(oldLayout)
def importFromDICOMWeb(dicomWebEndpoint,
studyInstanceUID,
seriesInstanceUID=None,
accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Progress is displayed and if errors occur then they are displayed in a popup window in the end.
If all the instances in a series are already imported then the series will not be retrieved and imported again.
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
Example: calling from PythonSlicer console
.. code-block:: python
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
"""
from dicomweb_client.api import DICOMwebClient
seriesImported = []
errors = []
clientLogger = logging.getLogger('dicomweb_client')
originalClientLogLevel = clientLogger.level
progressDialog = slicer.util.createProgressDialog(
parent=slicer.util.mainWindow(), value=0, maximum=100)
try:
progressDialog.labelText = f'Retrieving series list...'
slicer.app.processEvents()
if accessToken is None:
client = DICOMwebClient(url=dicomWebEndpoint)
else:
client = DICOMwebClient(
url=dicomWebEndpoint,
headers={"Authorization": f"Bearer {accessToken}"},
)
seriesList = client.search_for_series(
study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if seriesInstanceUID is not None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
# Turn off detailed logging, because it would slow down the file transfer
clientLogger.setLevel(logging.WARNING)
fileNumber = 0
cancelled = False
for seriesIndex, currentSeriesInstanceUID in enumerate(
seriesInstanceUIDs):
progressDialog.labelText = f'Retrieving series {seriesIndex+1} of {len(seriesInstanceUIDs)}...'
slicer.app.processEvents()
try:
seriesInfo = client.retrieve_series_metadata(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
numberOfInstances = len(seriesInfo)
# Skip retrieve and import of this series if it is already imported
alreadyImportedInstances = slicer.dicomDatabase.instancesForSeries(
currentSeriesInstanceUID)
seriesAlreadyImported = True
for serieInfo in seriesInfo:
sopInstanceUID = serieInfo['00080018']['Value'][0]
if sopInstanceUID not in alreadyImportedInstances:
seriesAlreadyImported = False
break
if seriesAlreadyImported:
seriesImported.append(currentSeriesInstanceUID)
continue
instances = client.iter_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime(
).toString("yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(
outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instanceIndex, instance in enumerate(instances):
progressDialog.setValue(
int(100 * instanceIndex / numberOfInstances))
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
filename = outputDirectoryPath + "/" + str(
fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
if cancelled:
# cancel was requested in instance retrieve loop,
# stop the entire import process
break
importDicom(outputDirectoryPath)
seriesImported.append(currentSeriesInstanceUID)
except Exception as e:
import traceback
errors.append(
f"Error importing series {currentSeriesInstanceUID}: {str(e)} ({traceback.format_exc()})"
)
except Exception as e:
import traceback
errors.append(f"{str(e)} ({traceback.format_exc()})")
finally:
progressDialog.close()
clientLogger.setLevel(originalClientLogLevel)
if errors:
slicer.util.errorDisplay(
f"Errors occurred during DICOMweb import of {len(errors)} series.",
detailedText="\n\n".join(errors))
elif cancelled and (len(seriesImported) < len(seriesInstanceUIDs)):
slicer.util.infoDisplay(
f"DICOMweb import has been interrupted after completing {len(seriesImported)} out of {len(seriesInstanceUIDs)} series."
)
return seriesImported
def importFromDICOMWeb(dicomWebEndpoint,
studyInstanceUID,
seriesInstanceUID=None,
accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Example usage:
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
"""
from dicomweb_client.api import DICOMwebClient
import random
progressDialog = slicer.util.createProgressDialog(
parent=slicer.util.mainWindow(), value=0, maximum=100)
progressDialog.labelText = f'Retrieving series list...'
slicer.app.processEvents()
if accessToken is None:
client = DICOMwebClient(url=dicomWebEndpoint,
callback=progressCallback)
else:
client = DICOMwebClient(
url=dicomWebEndpoint,
headers={"Authorization": f"Bearer {accessToken}"},
)
seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if not seriesInstanceUID is None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
fileNumber = 0
cancelled = False
for seriesIndex, currentSeriesInstanceUID in enumerate(seriesInstanceUIDs):
progressDialog.labelText = f'Retrieving series {seriesIndex+1} of {len(seriesInstanceUIDs)}...'
slicer.app.processEvents()
instances = client.retrieve_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
progressDialog.setValue(
int(100 * seriesIndex / len(seriesInstanceUIDs)))
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime().toString(
"yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(
outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instanceIndex, instance in enumerate(instances):
filename = outputDirectoryPath + "/" + str(fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
importDicom(outputDirectoryPath)
if cancelled:
break
progressDialog.close()
return seriesInstanceUIDs
